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Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.

Yadav VK, Thakur RK, Eckloff B, Baral A, Singh A, Halder R, Kumar A, Alam MP, Kundu TK, Pandita R, Pandita TK, Wieben ED, Chowdhury S - Nucleic Acids Res. (2014)

Bottom Line: These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown.For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF.Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy and do all TF binding and associated changes in nucleosome occupancy result in altered gene expression?

View Article: PubMed Central - PubMed

Affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.

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Nucleosome depletion and NME2 occupancy. (A) Schematic representation of possible relationship between nucleosome positions before and after inducing NME2. (B) Nucleosome occupancy is depleted on or near NME2 binding sites on inducing NME2 relative to the condition before NME2 induction. Ratio of number of nucleosomes detected after/before NME2 induction in 300 bp windows is shown; x-axis denotes the distance of nucleosomes from the nearest NME2 binding site in NME2-induced cells. (C) Schematic representation of nucleosome shift between two conditions was represented by ΔNdisplacement (left panel). Percentage of shifted nucleosomes plotted for a given ΔNdisplacement is shown in the right panel (x-axis was plotted to indicate: no shift, shift in 100 bp windows and shift exceeding 300 bases). Distribution of the nucleosome shift was also found for the NME2-depleted condition minus A549 cells; significance of the difference in distributions was tested using the Wilcoxon rank sum test (P = 0.00016). (D) Position of the nearest nucleosome with respect to NME2 binding sites in cells before (green) or after inducing NME2 (red; left panels); 791 genes where the nearest nucleosome was within 300 bp and shifted in the NME2-induced condition are shown. Expression level of corresponding genes in triplicate before or after NME2 induction is shown in the right panels.
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Figure 3: Nucleosome depletion and NME2 occupancy. (A) Schematic representation of possible relationship between nucleosome positions before and after inducing NME2. (B) Nucleosome occupancy is depleted on or near NME2 binding sites on inducing NME2 relative to the condition before NME2 induction. Ratio of number of nucleosomes detected after/before NME2 induction in 300 bp windows is shown; x-axis denotes the distance of nucleosomes from the nearest NME2 binding site in NME2-induced cells. (C) Schematic representation of nucleosome shift between two conditions was represented by ΔNdisplacement (left panel). Percentage of shifted nucleosomes plotted for a given ΔNdisplacement is shown in the right panel (x-axis was plotted to indicate: no shift, shift in 100 bp windows and shift exceeding 300 bases). Distribution of the nucleosome shift was also found for the NME2-depleted condition minus A549 cells; significance of the difference in distributions was tested using the Wilcoxon rank sum test (P = 0.00016). (D) Position of the nearest nucleosome with respect to NME2 binding sites in cells before (green) or after inducing NME2 (red; left panels); 791 genes where the nearest nucleosome was within 300 bp and shifted in the NME2-induced condition are shown. Expression level of corresponding genes in triplicate before or after NME2 induction is shown in the right panels.

Mentions: We next checked target-site nucleosome occupancy before and after NME2 induction (Figure 3A). On analyzing relative occurrence we found lower number of positioned nucleosomes in the vicinity (∼300–500 bp) of NME2 target sites in cells after NME2 induction (Figure 3B). Out of 3956 NME2 target sites (within −7.5 to +2.5 kb of TSS) unique to the NME2-induced cells, 1257 (31%) present on 1119 putative promoters were found to either overlap or were within 300 bases of a nucleosome in cells before NME2 induction. Furthermore, 870 (∼70%) of the 1257 sites were found to be nucleosome-free in the NME2-induced condition, which involved repositioning of 870 nucleosomes in 791 genes on NME2 induction. Together, these findings indicate that many of the NME2 binding sites occupied by nucleosomes in the un-induced condition in A549 cells became NME2-bound (and nucleosome-free) in the NME2-induced condition.


Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.

Yadav VK, Thakur RK, Eckloff B, Baral A, Singh A, Halder R, Kumar A, Alam MP, Kundu TK, Pandita R, Pandita TK, Wieben ED, Chowdhury S - Nucleic Acids Res. (2014)

Nucleosome depletion and NME2 occupancy. (A) Schematic representation of possible relationship between nucleosome positions before and after inducing NME2. (B) Nucleosome occupancy is depleted on or near NME2 binding sites on inducing NME2 relative to the condition before NME2 induction. Ratio of number of nucleosomes detected after/before NME2 induction in 300 bp windows is shown; x-axis denotes the distance of nucleosomes from the nearest NME2 binding site in NME2-induced cells. (C) Schematic representation of nucleosome shift between two conditions was represented by ΔNdisplacement (left panel). Percentage of shifted nucleosomes plotted for a given ΔNdisplacement is shown in the right panel (x-axis was plotted to indicate: no shift, shift in 100 bp windows and shift exceeding 300 bases). Distribution of the nucleosome shift was also found for the NME2-depleted condition minus A549 cells; significance of the difference in distributions was tested using the Wilcoxon rank sum test (P = 0.00016). (D) Position of the nearest nucleosome with respect to NME2 binding sites in cells before (green) or after inducing NME2 (red; left panels); 791 genes where the nearest nucleosome was within 300 bp and shifted in the NME2-induced condition are shown. Expression level of corresponding genes in triplicate before or after NME2 induction is shown in the right panels.
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Figure 3: Nucleosome depletion and NME2 occupancy. (A) Schematic representation of possible relationship between nucleosome positions before and after inducing NME2. (B) Nucleosome occupancy is depleted on or near NME2 binding sites on inducing NME2 relative to the condition before NME2 induction. Ratio of number of nucleosomes detected after/before NME2 induction in 300 bp windows is shown; x-axis denotes the distance of nucleosomes from the nearest NME2 binding site in NME2-induced cells. (C) Schematic representation of nucleosome shift between two conditions was represented by ΔNdisplacement (left panel). Percentage of shifted nucleosomes plotted for a given ΔNdisplacement is shown in the right panel (x-axis was plotted to indicate: no shift, shift in 100 bp windows and shift exceeding 300 bases). Distribution of the nucleosome shift was also found for the NME2-depleted condition minus A549 cells; significance of the difference in distributions was tested using the Wilcoxon rank sum test (P = 0.00016). (D) Position of the nearest nucleosome with respect to NME2 binding sites in cells before (green) or after inducing NME2 (red; left panels); 791 genes where the nearest nucleosome was within 300 bp and shifted in the NME2-induced condition are shown. Expression level of corresponding genes in triplicate before or after NME2 induction is shown in the right panels.
Mentions: We next checked target-site nucleosome occupancy before and after NME2 induction (Figure 3A). On analyzing relative occurrence we found lower number of positioned nucleosomes in the vicinity (∼300–500 bp) of NME2 target sites in cells after NME2 induction (Figure 3B). Out of 3956 NME2 target sites (within −7.5 to +2.5 kb of TSS) unique to the NME2-induced cells, 1257 (31%) present on 1119 putative promoters were found to either overlap or were within 300 bases of a nucleosome in cells before NME2 induction. Furthermore, 870 (∼70%) of the 1257 sites were found to be nucleosome-free in the NME2-induced condition, which involved repositioning of 870 nucleosomes in 791 genes on NME2 induction. Together, these findings indicate that many of the NME2 binding sites occupied by nucleosomes in the un-induced condition in A549 cells became NME2-bound (and nucleosome-free) in the NME2-induced condition.

Bottom Line: These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown.For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF.Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy and do all TF binding and associated changes in nucleosome occupancy result in altered gene expression?

View Article: PubMed Central - PubMed

Affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.

Show MeSH
Related in: MedlinePlus